Installation with pip fails

[tbridel]

Good evening,

I am working on a project involving the long-time integration of an ODE, and the results you show definitely look very promising, but I cannot install the package ...

I am working on mac os X v12.4 with a M1 chip.
Python v3.10.8, pip v22.3.1, setuptools v65.5.1.

To really test only the install of numbalsoda and remove all possible side effects from pre-installed packages, I put myself in a new virtualenv.
🔴 I am getting the following error when doing pip install numbalsoda:

pip install numbalsoda
Collecting numbalsoda
  Downloading numbalsoda-0.3.4.tar.gz (241 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 241.3/241.3 kB 2.8 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy
  Downloading numpy-1.23.5-cp310-cp310-macosx_11_0_arm64.whl (13.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.4/13.4 MB 9.5 MB/s eta 0:00:00
Collecting numba
  Downloading numba-0.56.4-cp310-cp310-macosx_11_0_arm64.whl (2.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 9.4 MB/s eta 0:00:00
Requirement already satisfied: setuptools in ./py3env/lib/python3.10/site-packages (from numba->numbalsoda) (65.5.1)
Collecting llvmlite<0.40,>=0.39.0dev0
  Downloading llvmlite-0.39.1-cp310-cp310-macosx_11_0_arm64.whl (23.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.1/23.1 MB 10.3 MB/s eta 0:00:00
Building wheels for collected packages: numbalsoda
  Building wheel for numbalsoda (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for numbalsoda (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [73 lines of output]
      /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/setuptools/dist.py:770: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
        warnings.warn(
      /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/setuptools/config/setupcfg.py:508: SetuptoolsDeprecationWarning: The license_file parameter is deprecated, use license_files instead.
        warnings.warn(msg, warning_class)
      
      
      --------------------------------------------------------------------------------
      -- Trying "Ninja" generator
      --------------------------------
      ---------------------------
      ----------------------
      -----------------
      ------------
      -------
      --
      Not searching for unused variables given on the command line.
      -- The C compiler identification is AppleClang 13.1.6.13160021
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang - skipped
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- The CXX compiler identification is AppleClang 13.1.6.13160021
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++ - skipped
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      -- Configuring done
      -- Generating done
      -- Build files have been written to: /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57/_cmake_test_compile/build
      --
      -------
      ------------
      -----------------
      ----------------------
      ---------------------------
      --------------------------------
      -- Trying "Ninja" generator - success
      --------------------------------------------------------------------------------
      
      Configuring Project
        Working directory:
          /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57/_skbuild/macosx-12.0-arm64-3.10/cmake-build
        Command:
          cmake /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57 -G Ninja -DCMAKE_INSTALL_PREFIX:PATH=/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57/_skbuild/macosx-12.0-arm64-3.10/cmake-install -DPYTHON_VERSION_STRING:STRING=3.10.8 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/Users/tbridel/Documents/1-CODES/py3env/bin/python -DPYTHON_INCLUDE_DIR:PATH=/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -DPYTHON_LIBRARY:PATH=/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/lib/libpython3.10.dylib -DPython_EXECUTABLE:PATH=/Users/tbridel/Documents/1-CODES/py3env/bin/python -DPython_ROOT_DIR:PATH=/Users/tbridel/Documents/1-CODES/py3env -DPython_INCLUDE_DIR:PATH=/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -DPython_FIND_REGISTRY:STRING=NEVER -DPython3_EXECUTABLE:PATH=/Users/tbridel/Documents/1-CODES/py3env/bin/python -DPython3_ROOT_DIR:PATH=/Users/tbridel/Documents/1-CODES/py3env -DPython3_INCLUDE_DIR:PATH=/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -DPython3_FIND_REGISTRY:STRING=NEVER -DCMAKE_MAKE_PROGRAM:FILEPATH=/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/ninja/data/bin/ninja -DSKBUILD=ON -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=12.0 -DCMAKE_OSX_ARCHITECTURES:STRING=arm64
      
      CMake Error at /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/cmake/data/share/cmake-3.25/Modules/CMakeDetermineFortranCompiler.cmake:33 (message):
        Could not find compiler set in environment variable FC:
      
        /usr/local/bin/gfortran.
      Call Stack (most recent call first):
        CMakeLists.txt:3 (project)
      
      
      CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage
      CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
      -- Configuring incomplete, errors occurred!
      See also "/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57/_skbuild/macosx-12.0-arm64-3.10/cmake-build/CMakeFiles/CMakeOutput.log".
      Traceback (most recent call last):
        File "/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/skbuild/setuptools_wrap.py", line 632, in setup
          env = cmkr.configure(
        File "/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/skbuild/cmaker.py", line 334, in configure
          raise SKBuildError(
      
      An error occurred while configuring with CMake.
        Command:
          cmake /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57 -G Ninja -DCMAKE_INSTALL_PREFIX:PATH=/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57/_skbuild/macosx-12.0-arm64-3.10/cmake-install -DPYTHON_VERSION_STRING:STRING=3.10.8 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/Users/tbridel/Documents/1-CODES/py3env/bin/python -DPYTHON_INCLUDE_DIR:PATH=/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -DPYTHON_LIBRARY:PATH=/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/lib/libpython3.10.dylib -DPython_EXECUTABLE:PATH=/Users/tbridel/Documents/1-CODES/py3env/bin/python -DPython_ROOT_DIR:PATH=/Users/tbridel/Documents/1-CODES/py3env -DPython_INCLUDE_DIR:PATH=/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -DPython_FIND_REGISTRY:STRING=NEVER -DPython3_EXECUTABLE:PATH=/Users/tbridel/Documents/1-CODES/py3env/bin/python -DPython3_ROOT_DIR:PATH=/Users/tbridel/Documents/1-CODES/py3env -DPython3_INCLUDE_DIR:PATH=/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -DPython3_FIND_REGISTRY:STRING=NEVER -DCMAKE_MAKE_PROGRAM:FILEPATH=/private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-build-env-tb3aezox/overlay/lib/python3.10/site-packages/ninja/data/bin/ninja -DSKBUILD=ON -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=12.0 -DCMAKE_OSX_ARCHITECTURES:STRING=arm64
        Source directory:
          /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57
        Working directory:
          /private/var/folders/8_/vb42yyg57lj90txl41w_m4ph0000gn/T/pip-install-s6p_6_f6/numbalsoda_aa6a60982d73407590bdf13f5c02eb57/_skbuild/macosx-12.0-arm64-3.10/cmake-build
      Please see CMake's output for more information.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for numbalsoda
Failed to build numbalsoda
ERROR: Could not build wheels for numbalsoda, which is required to install pyproject.toml-based projects

🔴 This error also occurs with numbalsoda v0.3.3.

🟢 The pip install runs fine for numbalsoda v0.2.1 however.

Could you please advise @Nicholaswogan ?

Thank you very much in advance !
Best,
T. Bridel-Bertomeu

[Nicholaswogan]

Hi! Can you try conda install -c conda-forge numbalsoda instead?

[tbridel]

Hey !

Thanks for the super fast answer !!

I am sorry I do not have anaconda installed on my machine ... :(
But ! Posting here made me realize that the error CMake is throwing is not that bad actually.

I could do

FC=/opt/homebrew/bin/gfortran pip install numbalsoda==0.3.4

and the install went through successfully.
So it is all good, sorry for the hurried issue report ! Feel free to close :)

And thanks for your reactivity again !

[tbridel]

P.S. : maybe you could consider adding a bit of logic to the CMakeLists to automatically locate the fortran compiler, even on a custom brew install ?

[Nicholaswogan]

I think CMake should be able to find fortran compilers in most cases. I'm not sure why yours was not found?

[tbridel]

Hey Nicholas,

It was a conflict with an old $FC env variable set to the wrong path for gfortran (from before Homebrew refactor). So it's all good, thanks for the support ! 🙏